Thông tin tài liệu
Overexpression and enzymatic characterization of
Neisseria
gonorrhoeae
penicillin-binding protein 4
Miglena E. Stefanova
1
, Joshua Tomberg
2
, Christopher Davies
3
, Robert A. Nicholas
2
and William G. Gutheil
1
1
Division of Pharmaceutical Sciences, University of Missouri-Kansas City, USA;
2
Department of Pharmacology, University of North
Carolina at Chapel Hill, North Carolina, USA;
3
Department of Biochemistry, Medical University of South Carolina, Charleston,
South Carolina, USA
The penicillin-binding proteins (PBPs) are ubiquitous bac-
terial enzymes involved in cell wall biosynthesis, and are the
targets of the b-lactam antibiotics. The low molecular mass
Neisseria gonorrhoeae PBP 4 (NG PBP 4) is the fourth PBP
revealed in the gonococcal genome. NG PBP 4 was cloned,
overexpressed, purified, and characterized for b-lactam
binding,
DD
-carboxypeptidase activity, acyl-donor substrate
specificity, transpeptidase activity, inhibition by a number of
active site directed reagents, and pH profile. NG PBP 4 was
efficiently acylated by penicillin (30 000
M
)1
Æs
)1
). Against a
setoffivea-ande-substituted
L
-Lys-
D
-Ala-
D
-Ala substrates,
NG PBP 4 exhibited wide variation in specificity with a
preference for N
e
-acylated substrates, suggesting a possible
preference for crosslinked pentapeptide substrates in the cell
wall. Substrates with an N
e
-Cbz group demonstrated pro-
nounced substrate inhibition. NG PBP 4 showed 30-fold
higher activity against the depsipeptide Lac-ester substrate
than against the analogous peptide substrate, an indication
that k
2
(acylation) is rate determining for carboxypeptidase
activity. No transpeptidase activity was apparent in a model
transpeptidase reaction. Among a number of active site-
directed agents, N-chlorosuccinimide, elastinal, iodoaceta-
mide, iodoacetic acid, and phenylglyoxal gave substantial
inhibition, and methyl boronic acid gave modest inhibition.
The pH profile for activity against Ac
2
-
L
-Lys-
D
-Ala-
D
-Ala
(k
cat
/K
m
) was bell-shaped, with pK
a
values at 6.9 and 10.1.
Comparison of the enzymatic properties of NG PBP 4 with
other
DD
-carboxypeptidases highlights both similarities and
differences within these enzymes, and suggests the possibility
of common mechanistic roles for the two highly conserved
active site lysines in Class A and C low molecular mass PBPs.
Keywords:
DD
-carboxypeptidase; penicillin-binding protein.
Penicillin-binding proteins (PBPs) are ubiquitous bacterial
enzymes that catalyze the last steps in cell wall biosynthesis
(reviewed in [1–5]), and are the targets of the b-lactam
antibiotics. In Gram-negative bacteria these enzymes cata-
lyze the reactions shown in Scheme 1. Each bacterial species
has a number of PBPs; for example, Escherichia coli has
eight classically known PBPs, labeled 1A, 1B, and 2–7, as
well as several recent additions including PBP 1C [6] and
PBP 6b [7]. PBPs have molecular masses of 20–120 kDa and
can be divided into two groups, the low molecular mass
(LMM) PBPs and the high molecular mass (HMM) PBPs
[3]. The LMM PBPs have a transpeptidase/hydrolase
domain whereas the HMM PBPs possess an additional
domain N-terminal to the PBP domain, which in some cases
catalyze a penicillin-insensitive transglycosylase reaction.
Different PBPs have different propensities for hydrolysis
and/or transpeptidase reactions [5]. HMM PBPs are often
the lethal targets for b-lactam antibiotics, whereas LMM
PBPs are not lethal targets. Two LMM PBPs have,
however, been found to play important roles in cell division
and cell shape; PBP 3 from Streptococcus pneumoniae is
required for normal septum formation [8], and PBP 5 from
E. coli is essential for normal cell shape [9].
Neisseria gonorrhoeae has only three PBPs visible on gels
when [
3
H]penicillin G-labeled membranes are analyzed by
SDS/PAGE and fluorography (PBPs 1, 2, and 3) [10].
Analysis of the recently completed genome sequences of
N. meningitidis [11] and N. gonorrhoeae (GenBank acces-
sion number AE004969) revealed a fourth gonococcal PBP,
termed PBP 4 (GenBank accession number AF156692).
PBPs 1 and 2 are HMM PBPs and are the major antibiotic
killing targets for N. gonorrhoeae [10]. PBP 1 is the gono-
coccal homologue of E. coli PBP 1A and likely catalyzes
both glycan polymerization and transpeptidation during cell
elongation [12]. PBP 2 is the homologue of E. coli PBP 3
and likely functions during cell division [13]. PBPs 3 and 4
are LMM PBPs, which are not lethal targets, and their role
in cell wall biosynthesis is unknown. In a recently completed
study, PBP 3 was found to be an exceptionally active
carboxypeptidase, and exhibited high rates of acylation by
Correspondence to W. G. Gutheil, Division of Pharmaceutical
Sciences, University of Missouri-Kansas City, 5005 Rockhill Road,
Kansas City, Missouri 64110.
Fax: +1 816 235 5190, Tel.: +1 816 235 2424,
E-mail: gutheilw@umkc.edu
Abbreviations: Alk-BSA, alkylated BSA; AR, Amplex
TM
Red; Boc,
tert-butoxycarbonyl; Caps, 3-(cyclohexyl amino)-1-propane sulfonic
acid; Cbz, carbobenzyloxy; CPase, carboxypeptidase; EC, Escherichia
coli; HMM, high molecular mass; LMM, low molecular mass; NG,
Neisseria gonorrhoeae;OPD,o-phenylenediamine; PBP, penicillin-
binding protein; KAA,
L
-Lys-
D
-Ala-
D
-Ala; TEA, triethylamine.
(Received 23 September 2003, accepted 21 October 2003)
Eur. J. Biochem. 271, 23–32 (2004) Ó FEBS 2003 doi:10.1046/j.1432-1033.2003.03886.x
b-lactam antibiotics. This study also found that deletion of
PBP 3 and PBP 4 individually had only a slight (P >0.05,
not statistically significant) effect on the growth and viability
of N. gonorrhoeae, whereas deletion of both resulted in a
modest (P < 0.05, statistically significant) decrease in rate
of cell growth. Moreover, scanning electron micrographs of
these cells revealed a change in morphology in cells lacking
both PBP 3 and PBP 4, but not in cells lacking only one of
these enzymes, suggesting a role for both enzymes in normal
cell wall biosynthesis [13a].
Characterization of PBPs in terms of enzymatic proper-
ties, structure/function relationships, and catalytic mechan-
ism [14,15] provides useful information for understanding
the role of individual PBPs in bacterial cell wall biosynthesis,
as well as a basis for the development of new inhibitors for
the PBPs [16] that could lead to the development of new
antibacterial agents. Enzymatic characterization efforts on
the PBPs have focused on LMM PBPs since in general only
LMM PBPs give detectable enzymatic activity, for reasons
which are as yet unclear. There are a number of similarities
between LMM and HMM PBPs in terms of active site
sequence [3] and architecture [14,17,18]. Both groups of
enzymes also act on cell wall peptidoglycan as their
substrate, and are reactive with b-lactam antibiotics.
Detailed studies of the LMM PBPs are therefore expected
to provide important information on the enzymological
properties of the PBP class of enzymes as a whole, and
information on the as yet unexplained functional and
catalytic differences between the LMM and HMM PBPs.
The present study reports the cloning, expression, puri-
fication, and enzymological characterization of N. gonor-
rhoeae (NG) PBP 4. NG PBP 4 was examined for b-lactam
binding,
DD
-carboxypeptidase activity, substrate specificity,
transpeptidase activity, sensitivity to general enzyme inhibit-
ors, and pH dependence. Comparison of the enzymatic
properties of NG PBP 4 with other
DD
-carboxypeptidases
highlights both similarities and differences within these
enzymes, and suggests the possibility of common mechan-
istic roles for the two highly conserved active site lysines in
Class A and C low molecular mass PBPs.
Experimental procedures
General materials and reagents
Tris,
D
-Ala, horseradish peroxidase (Type X; 21 mgÆmL
)1
as an ammonium sulfate suspension; 250 UÆmg
)1
), ampi-
cillin, FAD, o-phenylenediamine (OPD), diacetyl-
L
-Lys-
D
-Ala-
D
-Lac (Ac
2
-KA-
D
-Lac) and
D
-lactate dehydrogenase
were from Sigma Chemical Co. Pig kidney
D
-amino acid
oxidase (6.0 mgÆmL
)1
as an ammonium sulfate suspension;
12 UÆmg
)1
) was from Roche Molecular Biochemicals. The
PBP/
DD
-carboxypeptidase substrate diacetyl-
L
-Lys-
D
-Ala-
D
-Ala (Ac
2
-KAA) and substituted XY-KAA substrates
were synthesized using standard methods of solution phase
peptide synthesis [19,20]. Amplex
TM
Red (10-acetyl-3,7-
dihydroxyphenoxazine; AR) was from Molecular Probes
and the QuantaBlu
TM
substrate solution was from Pierce
Chemical Co. Protein content was determined by using the
Micro Bradford assay (Sigma) according to the manufac-
ture’s protocol. Alkylated BSA (Alk-BSA) was prepared as
described previously [15].
Cloning, expression and protein purification
The NG PBP 4 coding sequence was amplified from
N. gonorrhoeae strain FA1090 genomic DNA with primers
based on the GenBank sequence (accession number
AF156692). The up primer annealed to codons 29–36
inclusive and contained an in-frame BamHI site at its 5¢-end,
whereas the down primer annealed to the last seven codons
of the coding sequence and contained an EcoRI site at its
5¢-end. The amplified fragment was cloned into a modified
pMAL-C2 vector (New England Biolabs), which fused
PBP 4 with hexahistidine-tagged maltose-binding protein
via a linker sequence containing a cleavage site for Tobacco
Etch Virus protease. The sequence of the cloned insert was
identical to the sequence both from the GenBank entry for
NG PBP 4 and from the completed FA1090 genome
(accession numbers AF156692 and AE004969, respectively).
The fusion protein was induced with 0.1 m
M
isopropyl-
thio-b-
D
-galactoside in E. coli MC1061 cells and purified
from cell lysates on a nickel chelating column. The purified
fusion protein was cleaved with Tobacco Etch Virus
protease, and the digest was repurified on a nickel chelating
column. PBP 4 did not elute in the flow-through, but
instead eluted from the column in 15 m
M
imidazole, while
maltose-binding protein and uncleaved fusion protein eluted
Scheme 1. PBP-catalyzed transpeptidase and carboxypeptidase reac-
tions in E. c oli.
24 M. E. Stefanova et al. (Eur. J. Biochem. 271) Ó FEBS 2003
in 150 m
M
imidazole. Puried PBP 4 was estimated to be
> 95% pure by SDS/PAGE, and was stored at )80 C.
Determination of the acylation rate of NG PBP 4
by several b-lactam antibiotics
The reaction mechanism for the interaction of PBPs with
peptide and b-lactam antibiotics is:
E ỵ S !
K
0
ES !
k
2
E S !
k
3
E ỵ P 1ị
The constant k
2
/KÂ, which describes the formation of the
covalent acyl-enzyme complex at low (subsaturating) con-
centrations of b-lactams, was determined from time courses
with [
14
C]penicillin G essentially as described [21]. NG PBP 4
(48 lg, 1.2 nmol) was diluted into 150 lL binding buffer
(50 m
M
sodium phosphate pH 7.0, 10% glycerol) and mixed
with an equal volume of 100 l
M
[
14
C]penicillin G in binding
buffer. At timed intervals, 20-lL aliquots were removed,
mixedwith5 mL5%trichloroaceticacid(w/v),andincubated
on ice for 15 min. The acidied proteins were passed through
#30 glass ber lters (Schleicher and Schuell) and the lters
were washedtwice with5 mLeachof 1%trichloroacetic acid/
33% methanol. The lters were then air dried, placed in
scintillation vials with 3 mL Scinti-safe scintillation uid
(Fisher Scientic), and counted.
k
2
/KÂ constants for ampicillin and ceftriaxone were
determined by the competition method against [
14
C]peni-
cillin G [21]. A xed concentration of [
14
C]penicillin G of
0.5 l
M
and concentrations of the unlabeled antibiotics that
inhibited binding by % 50% were incubated with PBP 4 in
sodium phosphate buffer pH 7, at room temperature for
3 min and the level of radioactivity bound to the proteins
was quantied as described above. Equation (2) was used to
calculate k
2
/KÂ constants, where EC
0
and EC
U
represent the
amount of acyl-enzyme complex formed in the absence and
presence of the unlabeled antibiotic, respectively, and C
U
and C
L
are the concentrations of the unlabeled and labeled
antibiotic, respectively.
k
2
K
0
U
ẳ
k
2
K
0
L
EC
0
EC
U
ịC
L
EC
U
ịC
U
2ị
Enzyme activity assays
$
D
-Ala-
D
-Ala carboxypeptidase (CPase) activity was deter-
mined by uorescence-based detection of
D
-Ala in micro-
titer plate-based assays as described in detail previously
[15,22]. Assays (50 lL) were performed in 100 m
M
pyro-
phosphate, 100 m
M
NaCl, 0.5 mgặmL
)1
Alk-BSA, at
pH 8.5. PBP 4 was diluted in the same buffer, and added
to reactions to start assays. Activity against the depsipeptide
(ester) substrate Ac
2
-KA-
D
-Lac was determined by detec-
tion of
D
-Lac using
D
-lactate dehydrogenase as described
previously [23], but with assays performed in microtiter
plates and the NADH product measured uorimetrically
(excitation at 325 nm, emission at 465 nm).
D
-Lac was used
as a standard. Control experiments were performed with
PBP 4 in the absence of substrate, and substrate in
the absence of PBP 4. In the case of the
D
-Lac based
substrate which has a labile ester bond, a low level of
esterolysis was observed in control experiments minus
NG PBP 4, which was subtracted from experimental values
plus NG PBP 4.
The linearity of NG PBP 4 catalyzed reactions was
veried in a time course experiment. NG PBP 4 (105 n
M
)
wasaddedto10m
M
(subsaturating) Ac
2
-KAA in the
standard CPase assay mixture. Reactions were stopped at
various times by the addition of ampicillin to 50 lgặmL
)1
(135 l
M
) and the accumulation of the hydrolysis product
(
D
-Ala) was determined uorimetrically. No product (
D
-
Ala) was produced for the zero time point demonstrating
that this ampicillin concentration completely blocked PBP 4
activity. Additional preliminary experiments further dem-
onstrated that the apparent K
i
values for ampicillin and
penicillin G are in the low nanomolar range (data not
shown).
Transpeptidase assays
PBPs can catalyze hydrolysis and/or transpeptidase reac-
tions (Scheme 1). To determine the ability of NG PBP 4 to
catalyze transpeptidase reactions, a model transpeptidase
reaction was performed with 10 m
M
Ac
2
-KAA as the acyl
group donor and variable concentrations of glycine as the
acyl group acceptor [24,25]. NG PBP 4 was added to
175 n
M
and reactions run for 150 min before stopping by
addition of ampicillin. This relatively high NG PBP 4
concentration was sufcient to convert 5% of substrate to
products, which allowed accurate product determination by
HPLC. The large amount of
D
-Ala hydrolysis product
produced at this level of turnover was determined using low
sensitivity OPD-based microtiter plate assays described
previously [23,26]. Transpeptidase (Ac
2
-KAG) and hydro-
lysis (Ac
2
-KA) products were quantied by reverse-phase
HPLC on a C18 column (5 lm, 0.46 ã 25 cm) with a water/
acetonitrile gradient. The column was equilibrated in 100%
A. Gradient: 025% B in 15 min [A: 0.1% (v/v) triuoro-
acetic acid in water; C: 0.09% (v/v) triuoroacetic acid in
acetonitrile;B:30%A/70%C(v/v)].
Substrate specicity
L
-Lys-
D
-Ala-
D
-Ala (KAA) based substrates with various N
a
(X) and N
e
(Y) substituents were incubated with NG PBP 4
at increasing substrate concentrations (050 m
M
XY-
KAA). Data were analyzed by tting with the appropriate
equations by nonlinear regression using
BMDP
statistical
software (SPSS Science).
Effect of inhibitors and reagents
Inhibitors and reagents at 1 m
M
were incubated with the
enzyme (21 n
M
)for1hat25Cinanassaymixture
containing all components of the CPase assay except for the
substrate. Ac
2
-KAA was then added to the assay. Reactions
were stopped by the addition of developing reagent
containing AR and ampicillin as described above. The
activity of untreated enzyme was taken as 100%.
pH dependence and pH stability
The effect of pH on NG PBP 4 activity was studied and
data analyzed as described in detail previously [15]. Activity
ể FEBS 2003 N. gonorrhoeae PBP 4 (Eur. J. Biochem. 271)25
was assayed in a series of overlapping buffers at 50 m
M
buffer, 100 m
M
NaCl, 0.5 mgÆmL
)1
Alk-BSA pH 3.5–
12.25, with 10 m
M
Ac
2
-KAA as the substrate. A control
study was performed to determine the effect of pH on
NG PBP 4 stability, also as described previously [15].
Amino acid sequences
The amino acid sequences used in this study were from
the Swiss-Prot database. The accession numbers were:
NG PBP 3, O85665; NG PBP 4, Q9XBT7; E. coli (EC)
PBP 5, P04287; Streptomyces K15 PBP, P39042; TEM-1
b-lactamase, P00810.
Results
b-Lactam binding activity
The gene encoding NG PBP 4 was amplified from N. gon-
orrhoeae FA1090 DNA, expressed in E. coli and purified as
described in Experimental procedures. To verify that the
purified protein was indeed a PBP, we carried out penicillin-
binding assays with [
14
C]penicillin G. As shown in Table 1,
NG PBP 4 displayed a k
2
/K¢ acylation rate constant of
30 000
M
)1
Æs
)1
with [
14
C]penicillin G, and an even higher
constant (56 000
M
)1
Æs
)1
) with ceftriaxone. In addition to
these assays, NG PBP 4 activity was found to be completely
inhibited by 140 l
M
ampicillin used to stop
DD
-CPase
assays, and an apparent K
i
in the low nanomolar range was
observed in additional control experiments (data not
shown).
Substrate specificity
Most LMM PBPs are active as
DD
-carboxypeptidases.
NG PBP 4 was characterized against several $
D
-Ala-
D
-Ala
based peptide substrates, as summarized in Fig. 1 and
Table 2. For data following expected Michaelis–Menten
behavior nonlinear regression with the form of the Micha-
elis–Menten equation shown in Eqn (3) was used to obtain
values and standard errors (SE) for k
cat
and K
m
, and the
form of this equation shown in Eqn (4) to obtain the value
and SE for k
cat
/K
m
.
v=E
T
¼
k
cat
½S
K
m
þ½S
ð3Þ
v=E
T
¼
ðk
cat
=K
m
ÞÂK
m
½S
K
m
þ½S
ð4Þ
In the case of Boc-Cbz-KAA and Ac-Cbz-KAA substantial
substrate inhibition was observed (Fig. 1). In these two
cases, only the data points from 0 to peak activity were
Fig. 1. Substrate specificity of NG PBP 4. CPase activity was assayed
as described in the text using 35 n
M
NG PBP 4, and a reaction time of
90 min.
D
-Ala product was detected with QuantaBlu
TM
assays. j,
Boc-Cbz-KAA; r, Boc-Ac-KAA; s, Ac-C-KAA; n, Ac
2
-KAA; h,
Boc-H-KAA; d, Ac
2
-KA-
D
-Lac. (A) High activity range showing
activity against Ac
2
-KA-
D
-Lac. (B) Middle activity range. (C) Low
activity range.
Table 1. k
2
/K¢ values for b-lactam antibiotic binding to NG PBP 4.
Standard errors are given in parentheses.
b-Lactam antibiotic k
2
/K¢ (
M
)1
Æs
)1
)
[
14
C]Penicillin G 30 000 (2000)
Ampicillin 3800 (300)
Ceftriaxone 56 000 (3000)
26 M. E. Stefanova et al. (Eur. J. Biochem. 271) Ó FEBS 2003
included in the statistical analysis using Eqn (4). The k
cat
/K
m
values, which reflect the activity of the enzyme at subsat-
urating (low) substrate concentrations, were determined
using this analysis and are accurate. However, the apparent
K
m
values will be lower than the true K
m
values, as will the
k
cat
values. An effort to fit the full concentration profile to
several substrate inhibition models was attempted, including
noncompetitive and uncompetitive substrate inhibition
models. An uncompetitive model [Eqn (5), where K
is
is
the substrate inhibition constant] gave the best fit of
experimental data, but the standard errors for kinetic
parameters were high due to overlapping K
is
and K
m
values.
The k
cat
and K
m
values for these two substrates could
therefore not be resolved, and are not reported.
v=E
T
¼
k
cat
½S
K
m
þ½Sþ½S
2
=K
is
ð5Þ
Values for k
cat
and K
m
for Boc-Ac-KAA and Boc-H-KAA
also could not be obtained, in these cases due to the lack
of apparent substrate saturation. Since the possibility of
substrate inhibition also exists for the other two substrates,
Ac
2
-KAA and Ac
2
-KA-
D
-Lac, the values for k
cat
and K
m
reported in Table 2 are given as the apparent values, and are
the minimum values for these parameters ) the true values
could be higher. Values for kinetic parameters are also based
on the assumption that all enzyme is catalytically active.
NG PBP 4 showed highest activity (k
cat
/K
m
)withN
a
-
acetylated substrates. Replacement of the N
a
-acetyl group
with the bulky Boc group decreased activity. Lowest activity
was obtained for Boc-H-KAA, which has a free (unacyl-
ated) N
e
. NG PBP 4 demonstrated an order of magnitude
higher activity against Ac
2
-KA-
D
-Lac (1730
M
)1
Æs
)1
)than
against the analogous peptide substrate Ac
2
-KAA
(76
M
)1
Æs
)1
), with apparent values for K
m
essentially the
same (60 m
M
vs. 40 m
M
, respectively).
Transpeptidase activity
No transpeptidase product was observed for NG PBP 4
catalyzed transpeptidation reactions with glycine as the
transpeptidase acceptor and Ac
2
-KAA as the acyl group
donor. A constant amount of accumulated
D
-Ala with
increasing Gly concentration was also observed (data not
shown). These results demonstrate that NG PBP 4 does not
show transpeptidase activity in a model transpeptidase
reaction between Ac
2
-KAA and Gly.
pH optimum and stability
The pH dependence of k
cat
/K
m
for NG PBP 4 catalyzed
hydrolysis of Ac
2
-KAA is presented in Fig. 2A. NG PBP 4
gave a bell-shaped pH profile with an optimum in the range
7.5–9.0. Data from TEA buffers demonstrated anomalous
behavior and were excluded from the analysis for pK
a
values. The k
cat
/K
m
vs. pH data was analyzed to determine
the pK
a
values as described previously [15]. pK
a
values were
6.9 (SE ¼ 0.1) and 10.1 (0.1). No anomalous effect of
buffers other than TEA was observed, except for a slight
preference for Caps over carbonate buffers. NG PBP 4 was
fully stable at pH 5.25–12.25 for 60 min at 25 °C (Fig. 2B).
Fig. 2. Effect of pH on activity and stability of NG PBP 4. (A) pH-rate
(k
cat
/K
m
) profile for NG PBP 4 hydrolysis of Ac
2
-KAA. The NG PBP
4 concentration was 21 n
M
, and the reaction time was 75 min.
D
-Ala
was detected with AR based assays. n, Citrate; s, Pi; r, PPi; e, TEA;
d, CO
3
2–
; h, Caps. The solid line represents the best fit curve calcu-
lated as described in Materials and methods with values of pK
1
¼ 6.9
(0.1) and pK
2
¼ 10.1 (0.1). (B) pH stability profile of NG PBP 4.
Experimental conditions were as described above. Symbols are as in A.
Table 2. Kinetic constants for hydrolysis of
D
-Ala and
D
-Lac based
substrates by NG PBP 4. Standard errors are given in parentheses.
H, No substituent; KAA,
L
-Lys-
D
-Ala-
D
-Ala; NS, not available due to
lack of apparent substrate saturation. SI, not available due to substrate
inhibition.
Substrate
a
k
cat
/K
m
(
M
)1
Æs
)1
) K
m
(m
M
)
b
k
cat
(s
)1
)
b
Ac
2
-KAA 76 (2) 40 (2) 3.1 (0.1)
Ac-Cbz-KAA 60 (10) SI SI
Boc-Cbz-KAA 27 (4) SI SI
Boc-Ac-KAA 11.3 (0.2) NS NS
Boc-H-KAA 3.58 (0.04) NS NS
Ac
2
-KA-
D
-Lac 1730 (70) 60 (6) 100 (6)
a
The N
a
-substituent of Lys is given first, N
e
-substituent is given
second.
b
Minimum apparent value as discussed in text.
Ó FEBS 2003 N. gonorrhoeae PBP 4 (Eur. J. Biochem. 271)27
Effect of enzyme inhibitors and reagents
NG PBP 4 was fully inhibited by the oxidizing agent
N-chlorosuccinimide (Table 3). Cysteine modifying rea-
gents iodoacetamide and iodoacetic acid, and the arginine
modifying reagent phenylglyoxal significantly inhibited
enzyme activity (40–50%). Among serine protease inhibi-
tors only elastinal gave substantial inhibition, although
methyl boronic acid showed modest inhibition. Serine-
directed organic phosphates were ineffective as inhibitors.
None of the tested metal ions or chelators significantly
affected enzyme activity.
Discussion
NG PBP 4 was identified from the complete genomic
sequence of N. gonorrhoeae. Although NG PBP 4 is not
visible when [
3
H]penicillin G-labeled membranes are
analyzed by SDS/PAGE and fluorography [10], a significant
decrease in growth rate and accompanying morphological
abnormalities occurred only when both PBP 3 (the other
LMM PBP in N. gonorrhoeae) and PBP 4 were deleted
[13a], strongly suggesting that PBP 4 plays a role in cell wall
synthesis. In this study NG PBP 4 was cloned, overex-
pressed, purified, and characterized to provide data required
for mechanistic and structure–function correlations with
other PBPs, and to provide a basis for understanding the
possible physiological function of this enzyme.
As NG PBP 4 was not observed in [
3
H]penicillin G
labeled membranes [10], it was possible that this protein
does not bind b-lactam antibiotics. However, b-lactam
binding experiments demonstrated that NG PBP 4 does
bind [
14
C]penicillin G and several other b-lactam antibiotics
with reasonably high k
2
/K¢ acylation rate constants
(Table 1). Although the k
2
/K¢ value of [
14
C]penicillin G
with NG PBP 4 is lower than that determined for
NG PBP 3 (198 000
M
)1
Æs
)1
), it is considerably higher than
that of E. coli PBP 5, which has a k
2
/K¢ for [
14
C]penicillin G
of 390
M
)1
Æs
)1
[26a]. Moreover, NG PBP 4 was completely
inhibited by ampicillin at the 140 l
M
concentration used to
stop carboxypeptidase reactions (data not shown). The lack
of an observable band corresponding to NG PBP 4 in
[
3
H]penicillin G-labeled gonococcal membranes following
SDS/PAGE and fluorography therefore cannot be due to a
Table 3. Effect of general enzyme inhibitors and reagents on the carboxypeptidase activity of three LMM PBPs. NG PBP 4 data, this paper;
NG PBP 3 data, unpublished observations; EC PBP 5 data, [15].
Inhibitor/reagent
Residual activity (%)
SpecificityNG PBP 4 NG PBP 3 EC PBP 5
Blank (untreated enzyme) 100 100 100
PMSF 104 101 113 Ser protease
Methanesulfonyl fluoride 96 100 82 Ser protease
DIFP 103 100 78 Ser protease
Leupeptin 89 99 108 Ser, Cys protease
Elastinal 45 100 66 Ser protease
Boric acid 85 99 89 Ser protease
Phenylboronic acid 89 24 73 Ser protease
Methylboronic acid 76 92 100 Ser protease
pHMB 81 97 0 Cys
Tetranitromethane 106 93 100 Tyr, Cys
N-Ethylmaleimide 91 99 9 Cys
Iodoacetamide 56 98 83 Cys
Iodoacetic acid 59 101 96 Lys, Cys
N-Chlorosuccinimide 8 5 44 Met, Cys, Trp
Formaldehyde 95 104 44 Cys, Lys, His
Acetic anhydride 104 103 74 Lys
Methylacetimidate 105 97 95 Lys
Diethyl pyrocarbonate 109 104 90 Lys, His, Tyr
Ethyl trifluorothioacetate 104 102 91 Lys
EDTA 115 102 96 Metal chelator
1,10-Phenanthroline 102 97 96 Metal chelator
Phosphoramidon 100 105 99 Zn protease
2-Aminoethylphosphonic acid 99 103 96 alanine analog
Phenylglyoxal 47 79 109 Arg
ZnCl
2
104 103 97
CdCl
2
99 105 91
CaCl
2
107 105 87
CoCl
2
103 103 94
CuCl
2
92 104 95
MnCl
2
89 105 100
MgCl
2
99 106 97
28 M. E. Stefanova et al. (Eur. J. Biochem. 271) Ó FEBS 2003
lack of interaction with penicillin G, and suggests that
N. gonorrhoeae grown in culture expresses only a low level
of this protein. Unidentified PBPs with a role in cell wall
morphology have previously been observed in E. coli [27].
NG PBP 4 activity against the $
D
-Ala-
D
-Ala substrate
Ac
2
-KAA was fairly typical for a PBP with a k
cat
value of
3s
)1
, K
m
value of 3 m
M
, and k
cat
/K
m
of 80
M
)1
Æs
)1
(Table 2). NG PBP 4 demonstrated substantial variation
in its activity against a set of XY-
L
-Lys-
D
-Ala-
D
-Ala peptide
substrates and the depsipeptide substrate Ac
2
-
L
-Lys-
D
-Ala-
D
-Lac (Table 2, Fig. 1). For substituents on the N
e
of Lys,
Ac- or Cbz-substituted substrates gave highest activity
whereas the absence of either an Ac or Cbz group in Boc-H-
KAA was associated with lowest activity, indicating a
preference of NG PBP 4 for N
e
-acylated substrates. For
comparison (Table 4), NG PBP 3 demonstrated a similar
preference for N
e
-acylated substrates, but in contrast was
more active with bulky substituents on the N
a
-position, and
EC PBP 5 demonstrated a notable lack of significant
preference for any of these derivatives. The observation
that NG PBP 3 and NG PBP 4 show a preference for N
e
-
substituted substrates suggests that the preferred substrates
for both LMM neisserial PBPs would be crosslinked
pentapeptides in the cell wall.
PBP-catalyzed reactions proceed through an acyl-enzyme
intermediate (Scheme 2). Depsipeptide (peptide-ester) sub-
strates for the PBPs often show a large increase in reaction
rate over the homologous amide substrates [28]. Since both
the depsipeptide (Ac
2
-
L
-Lys-
D
-Ala-
D
-Lac) and amide (Ac
2
-
L
-Lys-
D
-Ala-
D
-Ala) substrates proceed through the same
acyl-enzyme intermediate (E-S in Scheme 2), k
3
will be the
same for both substrates. A greater turnover number (k
cat
)
for a depsipeptide substrate is therefore attributed to a
higher k
2
, and is an indication that k
2
(acylation) is the rate
determining step for hydrolysis of the peptide substrate
[28,29]. Conversely, if peptide and depsipeptide substrates
show similar turnover numbers then this is evidence that k
3
(deacylation) is rate determining. NG PBP 4 demonstrated
a much higher k
cat
(30-fold) against Ac
2
-
L
-Lys-
D
-Ala-
D
-Lac
than against Ac
2
-
L
-Lys-
D
-Ala-
D
-Ala (Ac
2
-KAA) (Table 2),
evidence that k
2
is rate determining for NG PBP
4-catalyzed hydrolysis of Ac
2
-KAA. Classic studies using
this approach demonstrated that k
2
is also rate determining
for EC PBP 5-catalyzed hydrolysis of Ac
2
-KAA [28]. In
contrast, deacylation (k
3
) appears rate limiting for both
NG PBP 3 [13a] and S. aureus PBP 4 [28,30] catalyzed
hydrolysis of amide and ester substrates.
A number of active site-directed inhibitors and metal ions
were tested for their ability to inhibit NG PBP 4 (Table 3).
N-chlorosuccinimide, elastinal, iodoacetamide, iodoacetic
acid, and phenylglyoxal gave substantial inhibition, and
methyl boronic acid gave modest inhibition. As there are no
cysteines in NG PBP 4, inhibition by iodoacetamide and
iodoacetic acid is attributed to lysine modification. Com-
parison with inhibitor data from NG PBP 3 and EC PBP 5
(Table 3) demonstrates that all three enzymes were largely
unaffected by general inhibitors of serine proteases, which is
noteworthy given the role of a serine acyl-enzyme interme-
diate in PBP catalysis [28]. This result is also consistent with
previous observations with the Streptomyces R61 carb-
oxypeptidase [31]. The only inhibitor effective against all
three enzymes was the oxidizing agent N-chlorosuccinimide
whichinhibitedfullyNGPBP4andNGPBP3,andtoa
substantial degree EC PBP 5 (Table 3). Thus, the PBPs
appear notably resistant to most active site-directed rea-
gents. In contrast, the PBPs appear generally sensitive to
transition state analogs such as peptide boronic acids [16]
and peptide phosphonates [32].
pH dependence is a fundamental enzyme characteristic
relevant to physiological, mechanistic, and kinetic under-
standing of enzyme catalyzed reactions [33]. The physio-
logical significance of pH dependence is of particular
relevance for the PBPs and the b-lactamases, which are
exposed to the extracellular environment. pH dependence of
N. gonorrhoeae growth and cell wall biosynthesis has been
investigated ([34] and references therein). N. gonorrhoeae
grows best at pH 7.2, with a growth window of 5.8–8.4.
There is a significant difference in N. gonorrhoeae growth
environment between the infected female and male, with the
vagina having a pH range of 4.2–7.5 and the male urethra
having a pH of 6.2–8.4. The pH dependence of NG PBP 4
(pK
a
values of 6.9 and 10.1) therefore overlaps the alkaline
side of the physiological growth range of N. gonorrhoeae in
both males and females, with better overlap with male
growth conditions. The pH profiles for NG PBP 3 and 4
are relatively acidic compared to that of EC PBP 5, which
further highlights the contrast between the pH profile of
EC PBP 5 (pK
a
values 8.2 and 11.1) and the physiological
growth range of E. coli (pH 6–8) [15]. This is especially
notable as EC PBP 5 is required for normal cell shape [9].
The pK
a
values for NG PBP 4 of 6.9 and 10.1 are almost
identical to the pK
a
values for NG PBP 3 of 6.8 and 9.8
[13a]. The pH profile of NG PBP 4, especially the acidic
limb, is also similar to the pH profile for the Class A TEM
b-lactamase with pK
a
values of 5.0–6.2 for the acidic limb
and 8.5 for the basic limb [35,36] (Table 5). The conserved
W-loop in Class A b-lactamases contains a highly conserved
Glu residue (Glu166) which is believed to act as the general
Scheme 2. PBP-catalyzed substrate hydrolysis.
Table 4. Enzyme activities (k
cat
/K
m
) for hydrolysis of
D
-Ala and
D
-Lac
based substrates by NG PBP 3, NG PBP 4 and EC PBP 5. NG PBP 4
data, this paper; NG PBP 3 data, [13a]; EC PBP 5 data, [15]. Stan-
dard errors are shown in parentheses.
Substrate
Enzyme activity (
M
)1
Æs
)1
)
NG PBP 4 NG PBP 3 EC PBP 5
Ac
2
-KAA 76 (2) 29 000 (2000) 12 (1)
Ac-Cbz-KAA 60 (10) 142 000 (6000) 12 (1)
Boc-Cbz-KAA 27 (4) 180 000 (30 000) 21 (1)
Boc-Ac-KAA 11.3 (0.2) 62 000 (6000) 9 (1)
Boc-H-KAA 3.58 (0.04) 8300 (400) 11 (1)
Ac
2
-KA-
D
-Lac 1730 (70) 12 300 (800) 700 (10)
a
a
[23].
Ó FEBS 2003 N. gonorrhoeae PBP 4 (Eur. J. Biochem. 271)29
base in the deacylation step of the catalytic cycle [37,38], and
it is considered responsible for the acidic limb (pK
a
5–6) in
the pH profile [35]. In contrast, EC PBP 5 contains an active
site loop spatially equivalent to the W-loop in b-lactamases
(W-like loop) but which lacks a suitably positioned Glu
residue [14]. Although His151 on the W-like loop of
EC PBP 5 aligns with Glu166 in TEM b-lactamase, this
residue does not appear properly oriented to participate in
catalysis [14] and the pK
a
values for EC PBP 5 carboxyp-
eptidase activity of 8.2 and 11.1 were assigned to Lys47
(SXXK motif) and Lys213 (KTG motif), respectively [15].
NG PBP 4 and NG PBP 3 are both Class C LMM
PBPs, for which no crystal structures are currently
available. At the sequence level, Class C LMM PBPs are
most similar to the Class A b-lactamases, followed by
Class A PBPs such as EC PBP 5 and the Streptomyces
K15 enzyme, followed by a relatively remote relationship
to the Class B LMM PBPs such as the Streptomyces R61
enzyme [39]. Both gonococcal enzymes are carboxypeptid-
ases, both have the highly conserved active site motifs
common to most members of this class of enzymes, and
both show a readily identifiable W-like loop motif in
sequence alignments (Table 6). However, assigning pK
a
values to specific residues in NG PBP 4 and NG PBP 3 is
difficult, especially in the absence of crystal structures. By
analogy with TEM b-lactamase and EC PBP 5, the basic
pK
a
of NG PBP 4 can be reasonably assigned to the KTG
motif lysine (Lys261) (Tables 5 and 6). The acidic limb of
NG PBP 4 at pH 6.9 is however, less easy to assign to
Lys102 and, at first glance, a residue with a more acidic
pK
a
would seem more appropriate. One such candidate is
Glu195, which is present on the W-like loop (Table 6). The
presence of a conserved Gly-Leu/Ile motif at the heart of
the W-like loop suggests that W-like loops may exhibit
similar structures within classes A and C of the LMM
PBPs. Indeed the main chain atoms of those for EC PBP 5
and the Streptomyces K15 transpeptidase can be super-
imposed with a root mean square deviation of 0.89 A
˚
.
If so, then Glu195 in NG PBP 4 is unlikely to be suitably
positioned to participate directly in catalysis.
The absence of other suitable candidates for the acidic
pK
a
in the active site, at least based on sequence
alignment data, focuses attention back to Lys102 as
potentially responsible for the acidic pK
a
. Such a low
pK
a
for a lysine would be unusual but not unprecedented
(e.g. acetoacetate decarboxylase, pK
a
5.9 [40]). A similar
argument also applies to NG PBP 3, and suggests Lys61
(SXXK motif) and Lys404 (KTG motif) as most likely
responsible for the acidic and basic pK
a
values, respect-
ively (Table 5). Most significantly, this assignment would
suggest the same mechanistic function of the two highly
conserved Lys residues in NG PBP 4 and NG PBP 3 as
in EC PBP 5 [14,15] and would support a common
mechanism of catalysis amongst class A and C LMM
PBPs.
Note added in proof: A recently reported structural and
mutagenesis study of the Streptomyces K15 PBP also
implicates the SXXK lysine as the catalytic base during
acylation [41].
Acknowledgements
Supported by NIH grants GM-60149 (WGG), AI-36901 (RAN), and
GM-066861 (CD). We thank Dr Ann E. Jerse for providing valuable
information and references on N. gonorrhoeae growth conditions
during review of this manuscript.
Table 6. Sequence alignment of amino acid residues in conserved motifs of NG PBP 3, NG PBP 4, EC PBP 5, TEM b-lactamase and Streptomyces
K15
DD
-transpeptidase. Conserved, mechanistically significant, or potentially mechanistically significant residues are shown in bold.
Protein
Motif
SXXK SXN X-(like) loop
(e. . .gl) KT(S)G
NG PBP 3
54 VNPASTMKLVT 64 294 DMNKRSDNLIA 304 343 VLENGSGLSRK 353 399 GLLRLKTGTLN 409
NG PBP 4 95 MPIASISKLMS 105 151 LSLMSSENRAT 161 192 RFYEPTGLNFQ 202 258 NIELQKTGYIR 266
EC PBP 5 40 RDPASLTKMMT 50 105 DINLQSGNDAC 115 146 HFQTVHGLDAD 156 210 NVDGIKTGHTD 218
Streptomyces K15 31 RSTGSTTKIMT 41 91 GLMLPSGCDAA 101 138 HFDSFDGIGNG 148 208 GAIGVKTGSGP 218
b-Lactamase 66 FPMMSTFKVLL 76 125 AAITMSDNTAA 136 162 LDRWEPELNEA 172 229 WFIADKSGAGE 239
Table 5. pK
a
values and residue assignments for TEM b-lactamase, EC PBP 5, NG PBP 3, and NG PBP 4. NA, data not available; AA, amino acid.
pK
a
Enzyme
TEM b-Lactamase EC PBP 5
a
NG PBP 3
b
NG PBP 4
c
pK
a
value AA residue pK
a
value AA residue pK
a
value AA residue pK
a
value AA residue
pK
1
5–6.2 Glu166
d
8.2 Lys47 6.8 Lys61? 6.9 Lys102?
pK
2
8.5 Lys234
e
11.1 Lys213 9.8 Lys404 10.1 Lys261
Anomalous buffers NA TEA, Carbonate TEA, Caps TEA
a
[15];
b
[13a];
c
this paper;
d
[35];
e
[36].
30 M. E. Stefanova et al. (Eur. J. Biochem. 271) Ó FEBS 2003
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-transpeptidase/penicillin-
binding protein probed by site-directed mutagenesis and structural
analysis. Biochemistry 42, 2895–2906.
32 M. E. Stefanova et al. (Eur. J. Biochem. 271) Ó FEBS 2003
. Overexpression and enzymatic characterization of
Neisseria
gonorrhoeae
penicillin-binding protein 4
Miglena E. Stefanova
1
,. the
vagina having a pH range of 4. 2–7.5 and the male urethra
having a pH of 6.2–8 .4. The pH dependence of NG PBP 4
(pK
a
values of 6.9 and 10.1) therefore overlaps
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